Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HDAC6

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF-7
cell type
ER+ breast cancer cells derived from pleural effusion of pt with breast adenocarcinoma
chip antibody
HDAC6 Cell Signaling Technology #7558
cell line
MCF-7
treatment
30 minutes 250 ng/mL prolactin, 120 minutes 0.1% DMSO

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Approximately 1.0 x 108 cells were used for each experimental condition and biological replicate (n=2 per condition and ChIP target). At the conclusion of ACY-241 treatment and/or prolactin stimulation, chromatin was cross-linked in 1% formaldehyde for 12 minutes, followed by neutralization with 1/20 volume of 2.5 M glycine. Cells were washed twice with ice-cold PBS, scraped and collected in a third volume of PBS, and briefly spun down before pellets were snap-frozen in liquid nitrogen. With the exception of sonication, which was performed using the Covaris M220 Focused-ultrasonicator (Covaris, Inc.), chromatin isolation, immunoprecipitation, and DNA extraction were performed as previously described [Lee, T.I., S.E. Johnstone, and R.A. Young, Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc, 2006. 1(2): p. 729-48]. DNA purity was assessed by spectrophotometry at 260, 270, and 280 nm, and integrity was assessed by capillary electrophoresis utilizing the Agilent 2100 Bioanalyzer. RNA-seq: RNA was extracted in phenol: chloroform: isoamyl alcohol (PCA) followed by ethanol precipitation. DNA was enzymatically digested prior to a second round of PCA and ethanol precipitation. RNA purity was assessed by spectrophotometry at 260, 270, and 280 nm, and integrity was assessed by capillary electrophoresis utilizing the Agilent 2100 Bioanalyzer. All samples possessed RIN (RNA Integrity Number) values ≥9. ChIP-seq: Library preparation was performed on ≥100 ng DNA using the Ovation Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN) according to the manufacturer's instructions. RNA-seq: Library preparation was performed on ≥500 ng RNA using the Universal Plus mRNA-Seq Library Preparation Kit (NuGEN) according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
6243961
Reads aligned (%)
82.4
Duplicates removed (%)
2.5
Number of peaks
943 (qval < 1E-05)

hg19

Number of total reads
6243961
Reads aligned (%)
81.5
Duplicates removed (%)
2.6
Number of peaks
881 (qval < 1E-05)

Base call quality data from DBCLS SRA